AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i216_aful_mthe_300.orf -o216_aful_mthe_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAG49065	70	Archaeoglobus_fulgidus
#2	RTH00518	35	M.thermo
#3	RTH01836	222	M.thermo
#4	RTH00222	184	M.thermo

Motif number 1

TCACCGTGAACTCCATGTGAGAAGAAACCT	3	63	0	CTCCATGTGA	    0.996358	-160
TCACATGGAGTTCACGGTGACATGAACATT	3	73	1	TTCACGGTGA	    0.896061	-150
TCGCTGTGAACTCCATGTGAAATGTTCATG	3	93	0	CTCCATGTGA	    0.996358	-130
TGGTGTTCATATCGCTGTGAACTCCATGTG	3	104	0	ATCGCTGTGA	     0.93936	-119
GCGATATGAACACCATATGATGAACCTCAG	3	119	1	CACCATATGA	    0.933652	-104
TGATGAACCTCAGAATGTGATATGCCGGTG	3	136	1	CAGAATGTGA	    0.944195	-87
AGAATGTGATATGCCGGTGAAAGATATATA	3	147	1	ATGCCGGTGA	    0.971632	-76
TGCCGCCCACCACCCTGTGACCTTTATATG	4	85	1	CACCCTGTGA	    0.994617	-100
TTATCCATCACTGCAGGTGAAACC      	4	171	1	CTGCAGGTGA	    0.991475	-14
          **********

Masking position 8
Map Score:   16.272

Number of sites scoring better than the average of aligned sites = 187
Number in coding regions = 178
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

CCATTACCGGTAATATGATCTGATAGGTTT	3	39	1	TAATATGATC	     0.82577	-184
TTTCTTCTCACATGGAGTTCACGGTGACAT	3	66	1	CATGGAGTTC	    0.981602	-157
GAACATTTCACATGGAGTTCACAGCGATAT	3	96	1	CATGGAGTTC	    0.981602	-127
AGGTTCATCATATGGTGTTCATATCGCTGT	3	116	0	TATGGTGTTC	    0.983841	-107
CATATCTAGATAATGAATTCAATTTTCAAC	4	22	0	TAATGAATTC	    0.792701	-163
TGAGGACCTATATTAAGATCCTCAATCATA	4	48	0	TATTAAGATC	    0.889402	-137
CTTAATTATATAAGGTGATCCCAACAATAG	4	134	1	TAAGGTGATC	    0.972907	-51
          **********

Masking position 2
Map Score:   6.15564

Number of sites scoring better than the average of aligned sites = 359
Number in coding regions = 337
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 3

ATCATATTACCGGTAATGGGAACAGGTGAG	3	28	0	CGGTAATGGG	    0.978826	-195
TGTGATATGCCGGTGAAAGATATATATACT	3	151	1	CGGTGAAAGA	    0.928653	-72
AAAGGTCACAGGGTGGTGGGCGGCAGATCC	4	80	0	GGGTGGTGGG	    0.994438	-105
ATATAATTAAGAGTGGTGGATGGGCTGTGC	4	115	0	GAGTGGTGGA	    0.986578	-70
GTTTCACCTGCAGTGATGGATAATCATTAA	4	164	0	CAGTGATGGA	    0.990018	-21
          **********

Masking position 4
Map Score:   3.29617

Number of sites scoring better than the average of aligned sites = 385
Number in coding regions = 364
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 4

TCATGTCACCGTGAACTCCATGTGAGAAGA	3	68	0	GTGAACTCCA	     0.99246	-155
TCATATCGCTGTGAACTCCATGTGAAATGT	3	98	0	GTGAACTCCA	     0.99246	-125
TCACAGCGATATGAACACCATATGATGAAC	3	114	1	ATGAACACCA	    0.977442	-109
ACACCATATGATGAACCTCAGAATGTGATA	3	128	1	ATGAACCTCA	    0.979152	-95
TATCTAGATAATGAATTCAATTTTCAACAA	4	20	0	ATGAATTCAA	    0.785693	-165
GACCTATATTAAGATCCTCAATCATATCTA	4	44	0	AAGATCCTCA	    0.809226	-141
ATTATATAAGGTGATCCCAACAATAGTTAA	4	138	1	GTGATCCCAA	    0.961043	-47
          **********

Masking position 4
Map Score:   8.16165

Number of sites scoring better than the average of aligned sites = 285
Number in coding regions = 270
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

GCTGGAGGCCCCTTCAAATCAAAAAAAGAA	2	14	0	CCTTCAAATC	    0.953204	-22
GAGAAGAAACCTATCAGATCATATTACCGG	3	45	0	CTATCAGATC	    0.961032	-178
ATATCTTTCACCGGCATATCACATTCTGAG	3	144	0	CCGGCATATC	    0.990635	-79
TTAAGATCCTCAATCATATCTAGATAATGA	4	36	0	CAATCATATC	    0.940981	-149
AGGGTGGTGGGCGGCAGATCCTTTGAGGAC	4	71	0	GCGGCAGATC	    0.978933	-114
          **********

Masking position 6
Map Score:   0.990368

Number of sites scoring better than the average of aligned sites = 131
Number in coding regions = 122
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 6

          **********

No masking
Map Score:   4.00336e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 7

          **********

No masking
Map Score:   4.00336e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 8

          **********

No masking
Map Score:   4.00336e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0